Related papers: Kinetic rates calculation via non-equilibrium dyna…
Protein-ligand interactions are crucial for a wide range of physiological processes. Many cellular functions result in these non-covalent `bonds' being mechanically strained, and this can be integral to proper cellular function. Broadly,…
Large parallel gains in the development of both computational resources as well as sampling methods have now made it possible to simulate dissociation events in ligand-protein complexes with all--atom resolution. Such encouraging progress,…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
This Feature Article presents an overview of the current status of Ring Polymer Molecular Dynamics (RPMD) rate theory. We first analyze the RPMD approach and its connection to quantum transition-state theory. We then focus on its practical…
A novel hybrid computational method based on the discrete-velocity (DV) approximation, including the lattice-Boltzmann (LB) technique, is proposed. Numerical schemes for the kinetic equations are used in regions of rarefied flows, and LB…
The development of machine-learning (ML) potentials offers significant accuracy improvements compared to molecular mechanics (MM) because of the inclusion of quantum-mechanical effects in molecular interactions. However, ML simulations are…
The impressive progress of the kinetic schemes in the solution of gas dynamics problems and the development of effective parallel algorithms for modern high performance parallel computing systems led to the development of advanced methods…
Analysis of bond rupture data from single-molecule force spectroscopy experiments commonly relies on the strong assumption that the bond dissociation process is irreversible. However, with increased spatiotemporal resolution of instruments…
Active plasma resonance spectroscopy (APRS) is a process-compatible plasma diagnostic method which utilizes the natural ability of plasmas to resonate on or near the electron plasma frequency. The Multipole Resonance Probe (MRP) is a…
We present a novel thermodynamically guided, low-noise, time-scale bridging, and pertinently efficient strategy for the dynamic simulation of microscopic models for complex fluids. The systematic coarse-graining method is exemplified for…
We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently-proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time Transition-State Theory (TST) limit is identical to…
Using molecular dynamics simulations, we determine the linear and nonlinear viscoelastic properties of a model polymer melt in the unentangled regime. Several approaches are compared for the computation of linear moduli, including…
This paper considers master equations for Markovian kinetic schemes that possess the detailed balance property. Chemical kinetics, as a prime example, often yields large-scale, highly stiff equations. Based on chemical intuitions, Sumiya et…
Accurate measurements of kinetic rate constants for interacting biomolecules is crucial for understanding the mechanisms underlying intracellular signalling pathways. The magnitude of binding rates plays a very important molecular…
During the past century, biologists and mathematicians investigated two mechanisms underlying bacteria motion: the run phase during which bacteria move in straight lines and the tumble phase in which they change their orientation. When…
Analytical formulas for effective drift, diffusivity, run times, and run lengths are derived for an intracellular transport system consisting of a cargo attached to two cooperative but not identical molecular motors (for example, kinesin-1…
Ring-polymer molecular dynamics (RPMD) has become a popular method for describing chemical reactions due to its ability to simultaneously capture tunneling, zero-point energy, anharmonicity and recrossing. Here we highlight that despite its…
Ring polymer molecular dynamics (RPMD) is used to directly simulate the dynamics of an excess electron in a supercritical fluid over a broad range of densities. The accuracy of the RPMD model is tested against numerically exact path…
Kinetic models of solid thermal decomposition are traditionally used for individual fit of isothermal decomposition experimental data. However, this methodology can provide unacceptable errors in some cases. To solve this problem, a neural…
Viscoelastic properties of polymer melts are particularly challenging to compute due to the intrinsic stress fluctuations in molecular dynamics (MD). We compared equilibrium and non-equilibrium MD approaches for extracting the storage (G')…